Contacts of the helix formed by residues 169 - 178 (chain A) in PDB entry 2JDQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.1 1.1 - - - +
165A VAL 3.5 0.2 + - - -
166A ILE 2.7 16.4 + - - -
167A GLN 3.1 2.6 - - - -
168A ALA* 1.3 79.5 - - - +
170A ALA* 1.3 61.1 + - - +
171A VAL 3.5 2.7 - - - -
172A PRO* 3.8 16.9 - - - +
173A ILE* 3.7 19.8 - - - +
206A TYR* 5.3 1.8 - - - -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.0 26.0 - - + -
135A LEU* 4.5 3.6 - - + -
151A LEU* 4.8 1.3 - - + -
165A VAL* 3.4 28.6 + - + +
166A ILE 4.1 0.4 + - - -
168A ALA 3.6 0.2 - - - -
169A GLY* 1.3 76.4 - - - +
171A VAL* 1.3 59.7 - - + +
173A ILE* 3.4 5.2 + - - +
174A PHE* 2.9 51.8 + - + -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.3 11.2 - - + +
170A ALA* 1.3 73.3 - - - +
172A PRO* 1.3 78.4 - - + +
174A PHE* 3.0 14.5 + - - +
175A ILE* 3.1 19.9 + - + +
193A LEU* 3.9 18.2 - - + -
196A ILE* 3.6 40.2 - - + -
206A TYR* 3.7 26.9 - - + -
207A VAL* 4.0 12.8 - - + -
210A CYS* 4.1 12.1 - - + -
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Residues in contact with PRO 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLY* 3.8 16.4 - - - +
171A VAL* 1.3 97.0 - - + +
173A ILE* 1.3 58.0 + - + +
175A ILE* 3.5 11.7 + - + +
176A GLU* 3.2 31.3 + - - +
206A TYR* 3.8 19.5 - - - +
210A CYS* 4.4 13.0 - - + +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.8 16.6 - - + +
135A LEU* 3.5 41.3 - - + +
136A LYS* 3.3 39.9 - - + +
169A GLY 3.7 16.8 - - - +
170A ALA* 3.4 7.7 + - - +
171A VAL 3.1 1.2 - - - -
172A PRO* 1.3 75.0 - - + +
174A PHE* 1.3 61.6 + - - +
176A GLU* 3.2 23.8 + - + +
177A LEU* 3.0 27.3 + - + +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.7 31.4 - - + -
148A ALA* 4.0 16.6 - - + -
151A LEU* 4.0 23.8 - - + -
165A VAL* 4.9 1.3 - - + -
170A ALA* 2.9 43.9 + - + +
171A VAL* 3.0 5.1 + - - +
173A ILE* 1.3 77.0 - - - +
175A ILE* 1.3 56.7 + - - +
177A LEU* 3.1 22.4 + - + +
178A LEU* 3.1 12.3 + - - +
189A ALA* 3.6 26.3 - - + +
192A ALA* 3.5 29.4 - - + -
193A LEU* 3.7 18.6 - - + -
196A ILE* 4.5 14.6 - - + -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.1 21.1 + - + +
172A PRO* 3.7 8.7 - - + +
174A PHE* 1.3 72.7 - - - +
176A GLU* 1.3 65.2 + - + +
178A LEU* 3.3 22.6 - - + +
179A SER* 4.2 2.3 + - - -
193A LEU* 4.0 12.3 - - + -
207A VAL* 4.1 1.3 - - + +
210A CYS* 3.3 41.3 - - + +
211A ASN 3.8 17.9 - - - +
212A ILE* 3.7 26.5 - - + -
215A PRO* 3.8 18.2 - - + +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS* 4.3 28.1 + - - +
172A PRO* 3.2 19.0 + - - +
173A ILE* 3.2 26.7 + - + +
175A ILE* 1.3 77.3 - - + +
177A LEU* 1.3 58.0 + - + +
179A SER* 3.0 28.7 + - - -
180A SER 3.8 0.2 + - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.7 41.7 - - + +
138A LYS* 4.6 12.8 - - + +
144A GLN* 3.0 29.2 - - - +
148A ALA* 5.3 1.1 - - + -
173A ILE* 3.0 17.4 + - + +
174A PHE* 3.1 20.4 + - + +
176A GLU* 1.3 73.3 - - + +
178A LEU* 1.3 60.1 + - - +
179A SER 3.0 2.0 - - - -
180A SER* 3.0 31.4 + - - -
185A VAL* 3.7 23.6 - - + -
186A GLN* 3.5 11.8 - - - -
189A ALA* 3.9 11.0 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE 3.1 15.3 + - - +
175A ILE* 3.3 15.7 - - - +
176A GLU 3.2 0.2 - - - -
177A LEU* 1.3 76.6 - - - +
179A SER* 1.3 52.3 + - - +
180A SER 3.4 0.9 - - - -
186A GLN* 2.8 38.0 + - - +
189A ALA* 4.4 1.3 - - + -
190A VAL* 3.4 40.4 - - + +
193A LEU* 4.2 6.5 - - + -
212A ILE* 3.9 27.4 - - + +
215A PRO* 4.0 20.5 - - + +
216A LEU* 3.9 24.5 - - + +
219A LEU* 3.8 14.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il